############################################################################## ############################################################################## ### ### Running command: ### ### E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:MultiAssayExperiment.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings MultiAssayExperiment_1.33.8.tar.gz ### ############################################################################## ############################################################################## * using log directory 'E:/biocbuild/bbs-3.21-bioc/meat/MultiAssayExperiment.Rcheck' * using R Under development (unstable) (2025-01-21 r87610 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.3.0 GNU Fortran (GCC) 13.3.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * using option '--no-vignettes' * checking for file 'MultiAssayExperiment/DESCRIPTION' ... OK * this is package 'MultiAssayExperiment' version '1.33.8' * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking whether package 'MultiAssayExperiment' can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking 'build' directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking code files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking dependencies in R code ... WARNING Missing or unexported object: 'HDF5Array::h5writeDimnames' * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking contents of 'data' directory ... OK * checking data for non-ASCII characters ... OK * checking data for ASCII and uncompressed saves ... OK * checking sizes of PDF files under 'inst/doc' ... OK * checking files in 'vignettes' ... OK * checking examples ... ERROR Running examples in 'MultiAssayExperiment-Ex.R' failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: HDF5MultiAssayExperiment > ### Title: Save a MultiAssayExperiment class object to HDF5 and Rds files > ### Aliases: HDF5MultiAssayExperiment saveHDF5MultiAssayExperiment > ### loadHDF5MultiAssayExperiment > > ### ** Examples > > > data("miniACC") > > testDir <- file.path(tempdir(), "test_mae") > > saveHDF5MultiAssayExperiment( + miniACC, dir = testDir, verbose = TRUE, replace = TRUE + ) Start writing assay 1/5 to HDF5 file: E:\biocbuild\bbs-3.21-bioc\tmpdir\RtmpGI1oKt/test_mae/miniACC_experiments.h5 / reading and realizing block 1/1 ... ok \ Writing it ... OK Finished writing assay 1/5 to HDF5 file: E:\biocbuild\bbs-3.21-bioc\tmpdir\RtmpGI1oKt/test_mae/miniACC_experiments.h5 Start writing assay 2/5 to HDF5 file: E:\biocbuild\bbs-3.21-bioc\tmpdir\RtmpGI1oKt/test_mae/miniACC_experiments.h5 / reading and realizing block 1/1 ... ok \ Writing it ... OK Finished writing assay 2/5 to HDF5 file: E:\biocbuild\bbs-3.21-bioc\tmpdir\RtmpGI1oKt/test_mae/miniACC_experiments.h5 Start writing assay 3/5 to HDF5 file: E:\biocbuild\bbs-3.21-bioc\tmpdir\RtmpGI1oKt/test_mae/miniACC_experiments.h5 / reading and realizing block 1/1 ... ok \ Writing it ... OK Finished writing assay 3/5 to HDF5 file: E:\biocbuild\bbs-3.21-bioc\tmpdir\RtmpGI1oKt/test_mae/miniACC_experiments.h5 Start writing assay 4/5 to HDF5 file: E:\biocbuild\bbs-3.21-bioc\tmpdir\RtmpGI1oKt/test_mae/miniACC_experiments.h5 / reading and realizing block 1/1 ... ok \ Writing it ... OK Finished writing assay 4/5 to HDF5 file: E:\biocbuild\bbs-3.21-bioc\tmpdir\RtmpGI1oKt/test_mae/miniACC_experiments.h5 Start writing assay 5/5 to HDF5 file: E:\biocbuild\bbs-3.21-bioc\tmpdir\RtmpGI1oKt/test_mae/miniACC_experiments.h5 / reading and realizing block 1/1 ... ok \ Writing it ... OK Finished writing assay 5/5 to HDF5 file: E:\biocbuild\bbs-3.21-bioc\tmpdir\RtmpGI1oKt/test_mae/miniACC_experiments.h5 Error: 'h5writeDimnames' is not an exported object from 'namespace:HDF5Array' Execution halted * checking for unstated dependencies in 'tests' ... OK * checking tests ... Running 'testthat.R' ERROR Running the tests in 'tests/testthat.R' failed. Last 13 lines of output: 1. └─MultiAssayExperiment::saveHDF5MultiAssayExperiment(...) at test-saveHDF5MultiAssayExperiment.R:113:5 2. └─MultiAssayExperiment:::.write_HDF5MultiAssayExperiment(...) 3. └─MultiAssayExperiment:::.write_h5_dimnames(assaylist, h5_path) 4. └─BiocGenerics::Map(...) 5. ├─BiocGenerics (local) standardGeneric("Map") 6. │ ├─BiocGenerics::eval(mc, env) 7. │ └─base::eval(mc, env) 8. │ └─base::eval(mc, env) 9. └─base::Map(f = f, ...) 10. └─base::mapply(FUN = f, ..., SIMPLIFY = FALSE) 11. └─MultiAssayExperiment (local) ``(dl = dots[[1L]][[1L]], al = dots[[2L]][[1L]]) [ FAIL 5 | WARN 40 | SKIP 1 | PASS 275 ] Error: Test failures Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 2 ERRORs, 1 WARNING See 'E:/biocbuild/bbs-3.21-bioc/meat/MultiAssayExperiment.Rcheck/00check.log' for details.